Highlighting parts of objects throughout animation
While you can animate the material colours as others have suggested you can also composite the change using masks.

Masks can be created in the Movie Editor for existing videos or in the UV/Image Editor if you just want to align a mask to the current render result or image. If your items were moving then you could animate the mask in the Movie Editor to follow the items, you can even parent them to motion tracked points instead of manually positioning each frame.



The bonus with compositing is that if you have already rendered the video or want to adjust an existing video it is much quicker than re-rendering the whole animation.